Fig. 2: Differentiation of binding specificity of intra-familiar proteins with the same binding motif. | Nature Communications

Fig. 2: Differentiation of binding specificity of intra-familiar proteins with the same binding motif.

From: Local DNA shape is a general principle of transcription factor binding specificity in Arabidopsis thaliana

Fig. 2

a, e Occurrence of the GTCGG(T/C) and C(G/T)TNNNNNNNAAG binding motifs in the A. thaliana genome sequence and the experimentally validated binding sequences of the AP2/EREBP TFs AT5G51990 and AT3G16280 and NAC TFs ANAC050 (AT3G10480) and BRN2 (AT4G10350). b, f Performance of the random forest regressor trained on the genomic 3D shape. Each line represents the ratio of correctly predicted binding sites regarding all validated binding sites for different affinity prediction cut-offs. The dark blue line corresponds to binding sequences which are bound by both TFs and the light blue lines correspond to the uniquely bound binding sequences. c The Venn diagrams show the sequence distributions according to the cut-off represented by the dashed line, respectively. Fields with light colours show the overlap of predicted and validated binding sequences. Dark coloured fields show the quantity of sequences, which were not predicted as bound by the model regarding the shown cut-off. d Influence of different local shape features on the prediction of the regressor model. The most influential features are at the top. Each row represents one shape feature at a single position within the sequence.

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